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30id

Recombinant Streptomyces plicatus EndoH

Method: X-RAY DIFFRACTION Dmax: 109.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Endo-beta-N-acetylglucosaminidase H

Streptomyces plicatus

UniProt P04067

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 48–312 Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1) Resolution 1.99 Å R-free 0.261
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 48–312 Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1) Resolution 1.99 Å R-free 0.261
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 48–312 Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1) Resolution 1.99 Å R-free 0.261
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 48–312 Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.2M Magnesium chloride, 0.1 M TRIS pH 8.5, 25% (w/v) PEG 3350 (Index H1) Resolution 1.99 Å R-free 0.261

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 30ID Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1C3F Endo-Beta-N-Acetylglucosaminidase H, D130N Mutant Deposited 1999-07-27 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：D130N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；17% PEG8000, 200 MM ZINC ACETATE 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.10 Å
1C8X Endo-Beta-N-Acetylglucosaminidase H, D130E Mutant Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：D130E PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；30% PEG1000, 100 MM CACODYLATE, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.00 Å
1C8Y Endo-Beta-N-Acetylglucosaminidase H, D130A Mutant Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：D130A ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% PEG1000, 100 MM ZN(AC)2, 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å
1C90 Endo-Beta-N-Acetylglucosaminidase H, E132Q Mutant Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：E132Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；19% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C90 Endo-Beta-N-Acetylglucosaminidase H, E132Q Mutant Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 48–312（265 aa）
Mutation：E132Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；19% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C91 Endo-Beta-N-Acetylglucosaminidase H, E132D Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：E132D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；15% PEG1000, 100 MM ZN(AC)2 100 MM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C92 Endo-Beta-N-Acetylglucosaminidase H, E132A Mutant Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：E132A No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；24% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1C93 Endo-Beta-N-Acetylglucosaminidase H, D130N/E132Q Double Mutant Deposited 1999-07-30 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 48–312（265 aa）
Mutation：D130N AND E132Q No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；34% PEG1500, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å
1EDT CRYSTAL STRUCTURE OF ENDO-BETA-N-ACETYLGLUCOSAMINIDASE H AT 1.9 ANGSTROMS RESOLUTION: ACTIVE SITE GEOMETRY AND SUBSTRATE RECOGNITION Deposited 1995-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 43–313（271 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
6VE1 Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH Deposited 2019-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 47–313（267 aa） Fragment：UNP residues 47-313
Chain D 47–313（267 aa） Fragment：UNP residues 47-313
Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 9；295 K；PEG20000, magnesium nitrate, TAPS, pH 9.0
Resolution 2.10 Å R-free 0.258
6VE1 Crystal structure of endo-beta-N-acetylglucosaminidase H at high pH Deposited 2019-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 47–313（267 aa） Fragment：UNP residues 47-313
Chain C 47–313（267 aa） Fragment：UNP residues 47-313
Not recorded MG MAGNESIUM ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；pH 9；295 K；PEG20000, magnesium nitrate, TAPS, pH 9.0
Resolution 2.10 Å R-free 0.258

9 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EBAG_STRPL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–266； UniProt 48–312 Author chain B； PDBConstruct 2–266； UniProt 48–312 Author chain C； PDBConstruct 2–266； UniProt 48–312 Author chain D； PDBConstruct 2–266； UniProt 48–312

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 30id

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 30id
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2. Structure Basics 2. Structure Basics

Entry ID entry_id30id
Deposition date deposition_date2026-04-28
最后修订 last_revision2026-05-13
Structure title titleRecombinant Streptomyces plicatus EndoH
Keywords keywordsglycosidase, TIM-barrel, APO, CARBOHYDRATE; CARBOHYDRATE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier33.69 Å
Radius of gyration Rg (electron density) rg_electron32.74 Å
Forward intensity I(0) i0211280000.00
Molecular weight molecular_weight114060.0 kDa
Excluded volume excluded_volume141550 ų
Envelope volume envelope_volume176980 ų
Hydration-shell volume shell_volume45017 ų
Envelope diameter envelope_diameter113.5 Å
Shell Rg shell_rg39.56 Å
Envelope Rg envelope_rg32.26 Å
Shape Rg shape_rg32.76 Å
Total Rg total_rg33.19 Å
Total atoms total_atoms15788
Residues n_residues1060
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax109.5 Å
Rg (real space) rg_real33.63 Å
Rg uncertainty (real space) rg_real_error0.96 Å
I(0) (real space) i0_real2.1130e+08
I(0) uncertainty (real space) i0_real_error3.8770e+06
Rg (reciprocal space) rg_reciprocal33.67 Å
I(0) (reciprocal space) i0_reciprocal211300000.0000
Solution quality estimate total_estimate0.8832
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary44.3 Å
Skewness Skewness skewness0.288
Kurtosis Kurtosis kurtosis-0.270
Angular range angular_range— – 0.2350 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha30330000.0000
Real-space data points n_real_points48
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.878; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.844
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)